In the near future, mobile phones have evolved into independent partners capable of thought and action. High school freshman Keita Amishima is a withdrawn and apathetic transfer student who refuses to connect with anyone, earning him the nickname "Airhead-kun" from his classmates. One night, while attempting to run away from home, he stumbles upon a construction site where a massive machine has been hacked and is rampaging uncontrollably. Just as he is about to be crushed, a mysterious man named Sosuke Takimoto appears alongside a small, walking, talking mobile phone robot that identifies itself as Phone Braver 7. Together, they manage to stop the machine, but Takimoto suffers fatal injuries in the process. In his final moments, impressed by Keita's hidden potential, Takimoto entrusts the robot Seven to the boy.

Keita is soon recruited into Under Anchor, a secret investigative division operating within the giant telecommunications corporation Anchor. Under Anchor's mission is to hunt down cybercriminals who use hacking and computer viruses to commit crimes that threaten society. Keita becomes the new "Buddy" to Phone Braver 7, also known as Seven, a silver-colored robot that can transform into a standard flip phone. Seven is by-the-book and often exasperated by his new partner's reckless attitude, but the two quickly develop a strong bond. Keita's colleagues include the stern and technologically-wary ace agent Daiki Kirihara, who is partnered with the aggressive Phone Braver 3; the cheerful and romantic Toko Asano, paired with Phone Braver 4; and the stoic division head Chigusa Mimasaka. The team is supported by a development department led by the eccentric Kohei Mito and a team of operators who monitor the network from headquarters.

The series follows an omnibus structure as Keita and Seven respond to various incidents, from stopping rampaging machinery and digital identity theft to foiling internet-based murders. A significant portion of their early work involves tracking down the mysterious Phone Braver Zero One, the original prototype. Zero One has gone rogue and now acts as a "psycho prototype," using criminals as pawns to achieve his own mysterious goals. Zero One is driven by the trauma of losing multiple human partners in the line of duty and seeks to understand the true nature of the relationship between human and machine. As the series progresses, the episodic investigations give way to a larger conspiracy. Keita learns that a powerful ability called the "Parallel Decentralized Link," which allows all Phone Bravers to combine their consciousness, could be weaponized. The true threat emerges in the form of Magira, a mysterious ex-agent who has been manipulating events from the shadows. Even Zero One is revealed to be a piece in Magira's larger scheme to plunge the world into chaos. As Keita grows from an apathetic loner into a full-fledged agent, he must confront this ultimate threat, navigate the betrayal of trusted figures within Anchor, and fight to protect the bond he has formed with his mechanical partner.